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Comment by akira2501 | Hacker News Reader

The cellular environment is such a mess it's not a surprise that environmental changes are observed by many types of bodies within the cell. It's hard to think of it like a "processor," though, when almost all of it's messages are non specific broadcasts and not direct targeted messages.

To me it seems like RNA is the processor, DNA is the RAM, and mitochondria are voltage regulation modules. That they're all environmentally sensitive is a consequence of how the machine is constructed.

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"To me it seems like RNA is the processor, DNA is the RAM,..."

Is there anything resembling a von Neumann machine in the biochemistry, though?

Would Turing machine analogues be more useful?

Both Turing and Von Neumann machines (and the lambda calculus by Church) were designed to be minimal implementations that were still powerful enough to be provably complete in a mathematical sense. Mother Nature is under no such constraints: she happily constructs massively parallel "computers" with millions of global variables, each being written to by every core. That human minds cannot debug such systems is not Her problem. The only constraint is if it works, and it does.

Epigenetic modifications, such as methylation, are made to DNA by specific proteins. These modifications alter the transcription process from DNA to RNA, which in turn affects protein expression. This includes the expression of the proteins responsible for epigenetic changes themselves. In essence, the proteins that modify DNA also control the expression of their own building instructions through a feedback loop.

I guess that feels a bit like a von neumann machine to me, but I'm not sure the analogy is super helpful.

Wouldn't RNA be the RAM and DNA be long term storage? Most of the work and "decision making" - at least in current organisms - is done by proteins.

There are many different types of RNA with different purposes. They all act in concert to produce proteins. mRNA encodes proteins, tRNA brings the proteins into transcription, rRNA actually acts as a protein itself to help drive this machine.

DNA is environmentally sensitive and it can be altered. Your entire genome is not being produced all the time. Different proteins are copied based upon the conformal structure of DNA which changes based upon the cellular environment. The entire structure is copied often and no one particular set of DNA in your body is "the original."

It has aspects of long term storage but then it's utilized in a way that long term storage almost never is. And all cells get their own copy which may be unique in several ways. So RAM seems like a better metaphor to me.

But aren't alterations confined to the epigenetic proteins found in chromatin? I may be mistaken but I thought the DNA itself stays the same while the epigenetic annotations change dynamically.

A long term storage that can also be used as a trap wire to catch pathogens.

[1]: https://en.wikipedia.org/wiki/Neutrophil_extracellular_traps

Given the billions of years of compression involved, these structures could occupy any number of latent spaces with all sorts of different meaning.

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